How about a post-fetch hook script that can do this? With an example of either printing a message or repacking in the background?
procmail includes a lockfile(1) utility useful for shell scripts, but it also wouldn't be hard to add a "git-lock-file <file> <command>..." utility that would create the given lock file, fork the command, and clean up again when it exited, relaying its exit status. (I can write one if there's interest.)
I agree with Linus that *defaulting* to background repack has problems, but it does seem useful to provide enough hooks to easily implement the option. Even printing the warning in a script seems like it would simplify internationalization, and different sites (e.g. reiserfs developers) might have different policies about what constitutes "a boatload".